As expected, phylogenetic analysis of a combined dataset comprising extant and reconstructed ancestral sequences (RAS) branched the latter at their node with near-zero branch lengths (not shown).
We checked that neither the mean nor the variance of species-specific estimated substitution rates are correlated to terminal branch lengths (not shown).
WT and Nrp2 +/− SGNs did not show differences in filopodial length (not shown), but Nrp2 +/− SGNs neurites did show a significant increase in the number of filopodial branches.
Although Maximum Likelihood inference yields the same branching order and similar branch lengths (tree not shown), the bootstrap support values for two of the three nodes associated with radiation of crested newt morphotypes (nodes II and III) are low (Table 2).
Simple neighbor-joining reconstructions based on uncorrected distances for both data sets (cytb and 'Brown region') revealed identical tree topologies and similar branch lengths (data not shown), indicating that both data sets contain solely mitochondrial fragments and no nuclear pseudogenes.
We also constructed a phylogenetic tree with concatenated protein coding gene sequences which exhibited the same topology as the one from the backbone sequence but with shorter branch lengths (data not shown).
If they were included in the alignment, these sequences cluster with LOTUSSLEEPER1, albeit with very long branch-length (data not shown).
BoNT/C infected and control neurons maintained a dense network of synapses on the timescale of this experiment No other morphological changes were observed in the BoNT/C infected cultures (neurite length, branching, not shown).
As different partitions showed branch length variation, we mapped branch lengths not significantly different from zero (at the α = 0.05 level) for 6/6 partitions, 5/6 partitions, 4/6 partitions, and no partitions onto our Bayesian consensus phylogram.
Stemminess (relative length of internal branches) increases when the longest branches are deleted (not shown), the best support in the interior of the network is that for Pancrustacea.
